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The arrest came after assistance from a member of the public who identified the alleged gunman.
The shooting occurred just after 9am at the Karapiro Café and Gifts shop on Tirau Rd (State Highway 1).
A man working in the shop was shot in the incident and is in a serious condition at Waikato Hospital.
The arrested man has been charged with wounding with intent to cause grievous bodily harm and will be appearing at the Hamilton District court tomorrow.
As the matter is before the courts police are unable to comment further.
Police said they were seeking information from the public after the shooting this morning.
"A caucasian male in his 50s or 60s has entered the shop and shot a man working there," Detective Senior Sergeant Matt Cranshaw said earlier today.
"Police believe the offender left the scene in a white or light-coloured older model vehicle which was being driven by a female."
A Waikato Hospital spokeswoman said the victim was in a very serious and critical condition in the high dependency unit.